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Crystal structure of MSMEG_1712 from Mycobacterium smegmatis in complex with Beta-D-Fucofuranose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 sodium chloride, magnesium chloride, Tris pH 7.5, PEG 1500
Crystal Properties Matthews coefficient Solvent content 3.12 60.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.065 α = 90 b = 118.065 β = 90 c = 232.2 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 PIXEL DECTRIS EIGER X 16M 2018-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 83.485 99.9 10.4 27.1 28372 63.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.512 2.806
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6HBD 2.5 52.62 1.35 19397 936 67.72 0.2123 0.2109 0.2113 0.2379 0.2349 70.73
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.4339 f_angle_d 1.389 f_chiral_restr 0.0701 f_bond_d 0.0103 f_plane_restr 0.0091
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4566 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing